Hello freesurfer experts,
I am trying to register a functional volumetric image (.nii) into a surface
(.gii) to produce a functional surface image (.gii), where each node of the
image will contain a time-series. My purpose for doing this is to use
freeview to visualize the time-series of each node. I've tried to do this
using bbregister to obtain a registration matrix of the functional image
into a structural image, mri_vol2surf to resample the functional volume, and
finally mris_convert to convert the resampled functional volume into a (4d)
functional surface. The details of how I used these commands are as follow:
bbregister --s AL_subject/AL \
--mov
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii \
--reg /home/osboxes/Desktop/AL_registrations/AL.mat \
--init-fsl --t2
mri_vol2surf --mov
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/AL/eyesshut_mc_bet.
feat/filtered_func_data.nii --reg
/home/osboxes/Desktop/AL_registrations/AL.mat --projfrac 0.5 --hemi lh --o
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh
--projfrac 0.5 --interp nearest
mris_convert -f
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.mgh \
/home/osboxes/Desktop/Windows-Share/EEG_fMRI_Data_CUBRIC/EEG_fMRI_FreeSurfer
_anatomies/AL_subject/AL/surf/lh.white \
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii
Although these commands run without any error, the result
(AL_surface_time_series_lh.gii) cannot be opened in freeview, presumably
because the produced 4d functional surface does not have the necessary
surface information (vertices, faces) needed by freeview in order to open
it. More specifically, when I try to open it I get MRISread failed
mriseadGIFTIfile: mris is NULL! found when parsing file
/home/osboxes/Desktop/AL_registrations/AL_surface_time_series_lh.gii in the
terminal.
I am new user of freesurfer and I would appreciate if someone could help me
with this.
Thanks,
Prokopis
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